Smith

Tree Position

Unique Mutations

The mutations unique to this man are summarized in the table below. Those with a '+' or '*' confidence level are considered by FamilyTreeDNA or FullGenomesCorp to be high quality SNPs/INDELs. For completeness, all other mutations of lesser confidence are included as well. These additional mutations may be useful for distinguishing between very closely related men.

Occasionally, some of the mutations listed here will be thought to be shared with other men in which case they might appear in upstream blocks on the tree. When this happens, the 'Blocks' field will indicate what block they appear in. Such a situation might arise with BigY men if the BED data suggests another man may be positive for a SNP, even though it doesn't appear in his VCF data. It might also happen if Chromo2 testing or Sanger sequencing of other men not on the tree show the SNP to be shared.

POSITION-REF-ALT (hg19)

Blocks

Names

Region

McDonald BED

combBED

STR

FTDNAN55408

FGCTDB0O

4048880-C-T

FGC19324

+

4633454-T-C

FGC19325

+

28578158-C-T

FGC19363

+

4745943-T-C

FGC19326

+

5543292-G-T

FGC19327

+

6925626-T-C

FGC19330

Y

Y

+

7127407-G-C

FGC19319

FGC19331

Y

Y

+

23103087-G-T

FGC19360

Y

+

23069454-G-A

M3846

Y

Y

+

+

7254938-G-A

FGC19332

Y

+

21864467-T-C

FGC19357

Y

Y

+

+

2665405-T-A

FGC19319

FGC19319

Y

Y

+

17982608-GATA-G

+

*

16564109-C-T

FGC19347

Y

Y

+

+

28709762-T-C

FGC19364

+

13684328-A-C

+

**

17850025-G-A

FGC19353

Y

Y

+

19081224-G-A

FGC19355

Y

Y

+

3973346-C-A

FGC19323

+

3597703-G-A

FGC19320

+

8845674-T-C

FGC19338

Y

Y

+

+

7815479-G-T

FGC19334

Y

Y

+

+

7785880-A-C

FGC19333

Y

Y

+

+

13548820-T-C

FGC19341

+

13684327-T-A

+

**

15770696-C-A

FGC19345

Y

Y

+

17683213-G-A

FGC19351

Y

+

3619084-A-G

FGC19321

*

5828807-A-G

FGC19328

*

3881489-C-T

FGC19322

*

14489855-C-A

CTS2796

Y

Y

*

16052579-GATAAATAA-G

8×ATAA

**

18780233-T-A

**

22258242-C-T

DYZ19

**

5096104-T-G

**

13129227-C-T

**

3374847-C-CAAAAAAA

23×A

**

14219767-G-GA

11×A

**

15012615-C-G

**

26500451-AACAC-A

P1_Y1

23×AC

**

2940686-G-C

**

18780234-C-T

**

13813964-ATGGACTCGAATGGAG-A

***

**

18994824-GGGAA-G

6×GGAA

***

**

18804474-A-AAGAG

26×AG

**

21929600-G-GTA

12×TA

**

19510264-C-CTTT

27×T

**

58877015-G-C

***

58880709-C-G

***

27305895-T-A

P1_g3

***

58877017-C-T

***

27305898-A-T

P1_g3

***

58869052-G-C

***

58890635-A-C

***

58867425-C-T

***

58865807-C-T

***

58863232-T-A

***

58859250-G-T

***

58890013-T-G

***

58826861-A-T

***

27305889-C-T

P1_g3

***

58890650-C-T

***

58859216-G-A

***

58898232-C-T

***

26379404-A-G

P1_Y1

***

26345378-C-A

P1_Y1

***

58908541-T-A

***

58909129-A-G

***

58909151-A-G

***

26345344-G-A

P1_Y1

***

26318315-C-T

P1_Y1

***

58909280-G-C

***

26247791-G-T

P1_Y1

***

25946401-T-A

P1_Y1

***

58894609-C-G

***

58857772-C-G

***

58857789-C-T

***

28103736-G-T

P1_Y2

***

58835951-G-T

***

58843750-A-C

***

58844912-A-T

***

58823532-A-T

***

58823471-C-T

***

58823199-G-A

***

58820205-A-T

***

58820192-T-G

***

58820181-T-C

***

28103768-C-T

P1_Y2

***

28103742-C-T

P1_Y2

***

28103740-A-T

P1_Y2

***

58845683-C-T

***

58857777-A-C

***

58846168-C-T

***

58847906-T-A

***

28103733-C-T

P1_Y2

***

27417794-A-C

P1_g3

***

58847928-T-C

***

58848010-G-A

***

58848304-G-A

***

58854222-C-G

***

58854392-C-G

***

58854782-C-T

***

27327894-A-T

P1_g3

***

58857766-C-T

***

58835838-A-G

***

13478482-G-T

***

13684327-TA-AC

***

58913269-A-G

***

22268151-ATGG-GTGA

DYZ19

***

17030992-CAAAAAA-C

19×A

***

17669700-CATAT-C

15×AT

***

18565061-C-CAAAA

27×A

***

18780233-TC-AT

***

19512249-CATATGTATTTATTTTGTAA-C

***

20252796-C-CAAAA

P5_Dst

24×A

***

20333835-C-CCGCAAAAAAAA

P5_Dst

24×A

***

20655022-ATGTG-A

P4_Prx

23×TG

***

21363090-CA-C

16×A

***

21853677-C-CAAAAAAA

43×A

***

22234462-GTA-ACT

DYZ19

***

22234486-AAAGTC-GAAATG

DYZ19

***

22257262-ATTTACGC-CTTTACGG

DYZ19

***

22365618-GC-TG

DYZ19

***

15491941-GTATATA-G

19×TA

***

22420627-CAGA-TAGG

DYZ19

***

22421683-TCC-AAG

DYZ19

***

23041233-G-AA

***

23084704-G-GTTTTTTT

19×T

***

23311272-CT-C

15×T

***

24686428-C-CTTTTT

P3_b2

23×T

***

26508369-GA-G

P1_Y1

***

27872479-G-GA

P1_Y2

10×A

***

58831552-CATTC-GATGA

***

58845112-ATTCAATTCCTTTCCA-T

***

58870564-T-TG

***

58877042-CTCGAA-TTCCAT

***

59007432-CTTT-C

18×T

***

59007959-C-CAAAAAAAAA

26×A

***

16768495-CAACAAC-AAAAAAA

***

14698458-C-CAAAAAAAAAAAAA

19×A

***

13203843-ACC-GTG

***

5235405-C-CTTTTT

31×T

***

21177056-T-TTA

11×TA

***

20815462-T-TAC

P4_Gap

12×AC

***

4134484-C-CA

18×A

***

13474008-CGTA-GGTT

***

2968166-GA-G

13×A

***

4236304-A-AAT

9×AT

***

13947521-G-GA

13×A

***

7155780-T-TA

14×A

***

3550569-C-AA

***

5178062-C-CA

20×A

***

25946363-G-A

P1_Y1

***

8660569-G-AA

***

2888870-C-CAAAAAAAA

32×A

***

5458125-CAA-C

16×A

***

13962042-C-CTTTTT

28×T

***

5778393-TGA-T

***

6473334-G-GA

13×A

***

7867879-GGAAAGAAAGAAAGAAA-G

16×GAAA

***

8575956-A-ATTTT

28×T

***

13203955-CATCATTATGG-GATAATGACGGT

***

13255410-GT-G

11×T

***

13445373-AAA-G

***

13453308-CCTTTCCATTG-C

***

13453379-CACTCGGGTTGATTCCATTCCTTTCCTATCCATTCT-C

***

13465631-AGC-TGA

***

13470330-T-TC

***

13470727-CGGA-TGGG

***

13487111-C-GCCT

***

13488968-CGGCCTGGG-TGGCGTGGA

***

25946396-C-A

P1_Y1

***

22456919-C-A

DYZ19

***

25946360-T-A

P1_Y1

***

13110570-C-A

***

6133856-C-G

***

6162299-A-C

IR3_Dst

***

6358141-C-T

***

9032382-G-C

***

9536340-C-A

IR3_Prx

***

9720740-A-G

IR3_Prx

***

9720743-C-G

IR3_Prx

***

9720752-T-A

IR3_Prx

***

9720801-T-A

IR3_Prx

***

13109969-C-T

***

13110043-G-C

***

13110089-A-G

***

13110127-T-A

***

13110584-C-A

***

2903298-C-T

***

13253750-C-G

***

13253924-T-C

***

13258690-G-C

***

13332909-G-A

***

13464190-T-G

***

13470298-T-C

***

13479734-G-A

***

13479781-T-C

***

13479794-T-G

***

13479802-G-C

***

13479802-G-A

***

13487115-A-C

***

13697720-C-A

***

13710303-T-A

***

4150894-T-G

***

22342796-A-T

DYZ19

***

16138803-G-A

P8_Dst

***

22332925-A-C

DYZ19

***

22164547-CA-C

19×A

***

22430155-T-C

DYZ19

***

13110094-A-C

A721

***

22481801-G-C

DYZ19

***

13467489-A-C

***

22488436-T-A

DYZ19

***

58910311-G-T

***

13456003-T-A,C

***

13479228-A-T

***

19735972-T-C

P5_Prx

***

22306375-A-G

DYZ19

***

23199656-C-G

***

24348659-G-C

P3_t1

***

26113823-T-TA

P1_Y1

***

2860458-G-GTTTTT

18×T

***

6162285-C-T

IR3_Dst

***

22293088-T-G

DYZ19

***

13251608-T-C

***

22337305-G-T

DYZ19

***

58845140-T-G

***

22420477-G-A

DYZ19

***

22421471-G-T

DYZ19

***

13258684-T-G

***

13258696-T-C

***

22337668-A-T

DYZ19

***

22337669-C-T

DYZ19

***

13258662-G-T

***

5308799-T-G

19×AG

***

4650522-C-T

***

13110088-C-G

***

13710347-G-T

***

16138811-T-A

P8_Dst

***

25876998-T-A

P1_Y1

***

22456963-A-G

DYZ19

***

22342626-A-G

DYZ19

***

22342731-G-T

DYZ19

***

22342754-T-G

DYZ19

***

22355186-G-A

DYZ19

***

22365130-A-T

DYZ19

***

22365221-G-A

DYZ19

***

22365576-G-A

DYZ19

***

22366637-G-T

DYZ19

***

22420655-T-G

DYZ19

***

22420672-G-C

DYZ19

***

22420691-G-C

DYZ19

***

22420710-G-C

DYZ19

***

22421675-A-T

DYZ19

***

22234913-C-G

DYZ19

***

22457124-C-T

DYZ19

***

22337416-C-G

DYZ19

***

22480658-A-G

DYZ19

***

22480659-T-C

DYZ19

***

22488419-G-A

DYZ19

***

25200789-G-A

g1

***

25289852-C-A

P2_r1

***

25430633-G-A

P2_r2

***

25805091-C-A

P1_b3

16×A

***

25854790-T-G

P1_Y1

***

25854896-A-C

P1_Y1

***

25854912-C-A

P1_Y1

***

25854917-A-T

P1_Y1

***

25854921-C-A

P1_Y1

***

25876953-A-G

P1_Y1

***

25876995-G-A

P1_Y1

***

22337438-C-T

DYZ19

***

22337415-C-A

DYZ19

***

16364111-T-C

11×AC

***

20326219-A-G

P5_Dst

***

18333573-G-T

P6_Prx

***

18438178-A-G

P6_Dst

***

18450112-C-T

P6_Dst

***

18483886-C-T

P6_Dst

***

19512530-T-A

***

19646199-T-C

P5_Prx

***

19763210-A-C

P5_Prx

***

19936314-A-T

P5_Prx

***

19936315-A-T

P5_Prx

***

19939023-C-T

P5_Prx

***

19939036-C-A

P5_Prx

***

20118040-C-T

P5_Dst

***

20118103-A-T

P5_Dst

***

20246019-G-A

P5_Dst

***

20338825-T-A

P5_Dst

***

22337385-T-A

DYZ19

***

20338826-C-A

P5_Dst

***

20452727-A-T

P5_Dst

***

20452779-G-C

P5_Dst

***

22234917-G-A

DYZ19

***

22234964-C-T

DYZ19

***

22236797-C-G

DYZ19

***

22236803-C-A

DYZ19

***

22252892-G-T

DYZ19

***

22252894-T-G

DYZ19

***

22257309-G-C

DYZ19

***

22273644-C-G

DYZ19

***

22309418-T-C

DYZ19

***

22335749-G-T

DYZ19

***

22336046-A-T

DYZ19

***

59013640-TTTTTT-ATATATA

***

In the table above, the meaning of the confidence field depends on whether the data comes from an FTDNA kit or an FGC kit. For FTDNA kits, + implies a "PASS" result with just one possible variant, * indicates a "PASS" but with multiple variants, ** indicates "REJECTED" with just a single variant, and *** indicates "REJECTED" with multiple possible variants. For FGC kits, + indicates over 99% likely genuine (95% for INDELs); * over 95% likely genuine (90% for INDELs); ** about 40% likely genuine; *** about 10% likely genuine. Manual entries read directly from a BAM file will be either + indicating positive, or * indicating that the data show a mixture of possible variants.

For the FTDNA kits, the BED data is encoded in the background color of the cells. Those cells with a white background have coverage, those with a grey background indicate no coverage in the BED file, and those with a pink background indicate the mutation is on the edge of a coverage region. These pink regions often indicate that the individual may be positive for a SNP even if there is no corresponding entry in the vcf file.

The McDonald BED column indicates whether or not the mutation is a SNP and falls in the BED region used by Dr. Iain McDonald in the age analysis he does for R-U106 men.

Haplotype Progression

The data below reveals the progression of changes in the haplotype. The bottom row is the haplotype for this man and above him are the inferred ancestral haplotypes for various upstream blocks. These inferred haplotypes are very much a work in progress, and any suggested modifications are appreciated. I think we can use our vast collection of haplotype data to refine these haplotypes. Mutations made from each upstream block are shown in sequence. The cell color is determined by the block in which the mutation took place.